マイクロサテライト イデンシ ザ ヲ リヨウ シタ ニホンサン ハーバーシール ノ コタイ シキベツホウ

近年では，糞，毛，羽などから遺伝情報が得られるようになり，銃やボーガンを使用して，遠距離から非直接的なサンプルが取れるようにもなった。しかし，このようなサンプルは，同一個体から複数回サンプリングしてしまう可能性があるため，遺伝子による個体識別が必要不可欠である。遺伝子を利用した個体識別は，一般的に複数のマイクロサテライト遺伝子座を使って行われる。個体識別に必要な遺伝子座とその数は，事前に既知のデータから遺伝子座ごとに重複率（PID : probability of identity）PID（obs）を算出して決定しておくことが望ましい。しかし，サンプル数が多く手に入らない場合，得られたサンプルの範囲内で予測値を推定する方法がある。PIDの予測値には，ハーディー・ワインベルグ平衡下の集団で血縁のない個体間の重複率（PID（theo））と，兄弟関係にある個体間の重複率（PID（sib））があり，実際の集団の重複率は，PID（theo）を下限，PID（sib）を上限と2つの予測値の間に位置するため，多くの動物では，PID（sib）の利用が推奨されている。本研究では，先行研究で集団が分かれることが示唆されているえりもと道東のハーバーシール2集団で，別個体と判明しているサンプルを基にPID（obs）と，2つの予測値を比較し，個体識別に必要な遺伝子座および遺伝子座数，予測値を算出するのに必要なサンプル数を決定した。その結果，日本のハーバーシールのPID（obs）は，PID（theo）とほぼ同等の値であり，4遺伝子座の使用で個体識別が可能であることを示した。一方で，個体識別に適した遺伝子座は，えりもと道東で異なった。さらに，日本のハーバーシールでは，20サンプルからPID（theo）を算出すれば，個体識別に有用な遺伝子座数の決定が行えることが示唆された。In recent years, genetic information has became much easier to obtain from feaces, hairs and feathers, and samples can be taken remotely by using biopsy darts fitted in guns and bowgun. Individual identification based on genetic information is crucial when using these non-distructive samples to avoid duplicate collection from single individuals, which may easily happen. In general, multiple microsatellite loci are used for individual identification. It is preferable that combination and the number of loci used for the analysis are decided using known individuals by calculating the proportion of all possible pairs of individuals that have the same genotypes (PID : probability of identity). However, if one does not have enough number of samples beforehand, theoretical estimator can be calculated using available samples. Theoretical PID assumes the population is in Hardy-Weinberg equilibrium and there are equations for unrelated individuals (PID(theo)) and siblings (PID(sib)). Since the observed PID generally lies between PID(theo) (lower boundary) and PID(sib) (upper boundary), it is recommended to use PID(sib) in many terrestrial animals. In this study, we calculated observed PID (PID(obs)) and two theoretical PIDs for two genetically distinct populations of Japanese harbour seals, Erimo and eastern Hokkaido, using the samples that are known to be from different individuals. Three PIDs are then compared, and combinations and numbers of loci essential for individual identification were investigated. The number of samples required for estimating PID are also investigated by picking different numbers of samples randomly for 100 times. The results of estimation indicated that PID(obs) for Japanese harbour seals showed similar values to PID(theo), and that at least 4 loci are required for identification. On the other hand, the loci useful for individual identification in Erimo and Eastern Hokkaido differed. Furthermore, it was suggested that 20 samples are enough to estimate PID(theo) and to detect loci useful for individual identification

Gene Organization in Rice Revealed by Full-Length cDNA Mapping and Gene Expression Analysis through Microarray

Rice (Oryza sativa L.) is a model organism for the functional genomics of monocotyledonous plants since the genome size is considerably smaller than those of other monocotyledonous plants. Although highly accurate genome sequences of indica and japonica rice are available, additional resources such as full-length complementary DNA (FL-cDNA) sequences are also indispensable for comprehensive analyses of gene structure and function. We cross-referenced 28.5K individual loci in the rice genome defined by mapping of 578K FL-cDNA clones with the 56K loci predicted in the TIGR genome assembly. Based on the annotation status and the presence of corresponding cDNA clones, genes were classified into 23K annotated expressed (AE) genes, 33K annotated non-expressed (ANE) genes, and 5.5K non-annotated expressed (NAE) genes. We developed a 60mer oligo-array for analysis of gene expression from each locus. Analysis of gene structures and expression levels revealed that the general features of gene structure and expression of NAE and ANE genes were considerably different from those of AE genes. The results also suggested that the cloning efficiency of rice FL-cDNA is associated with the transcription activity of the corresponding genetic locus, although other factors may also have an effect. Comparison of the coverage of FL-cDNA among gene families suggested that FL-cDNA from genes encoding rice- or eukaryote-specific domains, and those involved in regulatory functions were difficult to produce in bacterial cells. Collectively, these results indicate that rice genes can be divided into distinct groups based on transcription activity and gene structure, and that the coverage bias of FL-cDNA clones exists due to the incompatibility of certain eukaryotic genes in bacteria

Phosphorylation-Independent Regulation of Atf1-Promoted Meiotic Recombination by Stress-Activated, p38 Kinase Spc1 of Fission Yeast

BACKGROUND:Stress-activated protein kinases regulate multiple cellular responses to a wide variety of intracellular and extracellular conditions. The conserved, multifunctional, ATF/CREB protein Atf1 (Mts1, Gad7) of fission yeast binds to CRE-like (M26) DNA sites. Atf1 is phosphorylated by the conserved, p38-family kinase Spc1 (Sty1, Phh1) and is required for many Spc1-dependent stress responses, efficient sexual differentiation, and activation of Rec12 (Spo11)-dependent meiotic recombination hotspots like ade6-M26. METHODOLOGY/PRINCIPAL FINDINGS:We sought to define mechanisms by which Spc1 regulates Atf1 function at the ade6-M26 hotspot. The Spc1 kinase was essential for hotspot activity, but dispensable for basal recombination. Unexpectedly, a protein lacking all eleven MAPK phospho-acceptor sites and detectable phosphorylation (Atf1-11M) was fully proficient for hotspot recombination. Furthermore, tethering of Atf1 to ade6 in the chromosome by a heterologous DNA binding domain bypassed the requirement for Spc1 in promoting recombination. CONCLUSIONS/SIGNIFICANCE:The Spc1 protein kinase regulates the pathway of Atf1-promoted recombination at or before the point where Atf1 binds to chromosomes, and this pathway regulation is independent of the phosphorylation status of Atf1. Since basal recombination is Spc1-independent, the principal function of the Spc1 kinase in meiotic recombination is to correctly position Atf1-promoted recombination at hotspots along chromosomes. We also propose new hypotheses on regulatory mechanisms for shared (e.g., DNA binding) and distinct (e.g., osmoregulatory vs. recombinogenic) activities of multifunctional, stress-activated protein Atf1

Meiotic Recombination Hotspots of Fission Yeast Are Directed to Loci that Express Non-Coding RNA

Polyadenylated, mRNA-like transcripts with no coding potential are abundant in eukaryotes, but the functions of these long non-coding RNAs (ncRNAs) are enigmatic. In meiosis, Rec12 (Spo11) catalyzes the formation of dsDNA breaks (DSBs) that initiate homologous recombination. Most meiotic recombination is positioned at hotspots, but knowledge of the mechanisms is nebulous. In the fission yeast genome DSBs are located within 194 prominent peaks separated on average by 65-kbp intervals of DNA that are largely free of DSBs.). Furthermore, we tested and rejected the hypothesis that the ncRNA loci and DSB peaks localize preferentially, but independently, to a third entity on the chromosomes.Meiotic DSB hotspots are directed to loci that express polyadenylated ncRNAs. This reveals an unexpected, possibly unitary mechanism for what directs meiotic recombination to hotspots. It also reveals a likely biological function for enigmatic ncRNAs. We propose specific mechanisms by which ncRNA molecules, or some aspect of RNA metabolism associated with ncRNA loci, help to position recombination protein complexes at DSB hotspots within chromosomes

Genes Involved in Systemic and Arterial Bed Dependent Atherosclerosis - Tampere Vascular Study

BACKGROUND: Atherosclerosis is a complex disease with hundreds of genes influencing its progression. In addition, the phenotype of the disease varies significantly depending on the arterial bed. METHODOLOGY/PRINCIPAL FINDINGS: We characterized the genes generally involved in human advanced atherosclerotic (AHA type V-VI) plaques in carotid and femoral arteries as well as aortas from 24 subjects of Tampere Vascular study and compared the results to non-atherosclerotic internal thoracic arteries (n=6) using genome-wide expression array and QRT-PCR. In addition we determined genes that were typical for each arterial plaque studied. To gain a comprehensive insight into the pathologic processes in the plaques we also analyzed pathways and gene sets dysregulated in this disease using gene set enrichment analysis (GSEA). According to the selection criteria used (>3.0 fold change and p-value <0.05), 235 genes were up-regulated and 68 genes down-regulated in the carotid plaques, 242 genes up-regulated and 116 down-regulated in the femoral plaques and 256 genes up-regulated and 49 genes down-regulated in the aortic plaques. Nine genes were found to be specifically induced predominantly in aortic plaques, e.g., lactoferrin, and three genes in femoral plaques, e.g., chondroadherin, whereas no gene was found to be specific for carotid plaques. In pathway analysis, a total of 28 pathways or gene sets were found to be significantly dysregulated in atherosclerotic plaques (false discovery rate [FDR] <0.25). CONCLUSIONS: This study describes comprehensively the gene expression changes that generally prevail in human atherosclerotic plaques. In addition, site specific genes induced only in femoral or aortic plaques were found, reflecting that atherosclerotic process has unique features in different vascular beds

Can a Non-Native Speaker Teacher Teach Engish in Japan?

English is vigorously learned in Japan, but the average level of English pro ciency of Japanese students is still low compared to that of other developed countries. This article will consider the purpose and signi cance of learning English for Japanese at the college level, based on the author’s experience, both as a student and a teacher, at Kyoto University, Japan. The English taught in Japanese universities, at present just as 40 years ago, has a tendency to be a humanities subject and thus make light of oralaural elements. This trait, rooted in the teachers’ general lack of &uency and a false notion that spoken English is void of content, and therefore inferior to written English, needs improvement. It is the responsibility of those involved in higher education to help each student to harbour rich content by cultivating robust thinking and motivate expression. English classes are mostly taught using Japanese, which also needs serious reconsideration. Considering Japan’s place both from the global and East-Asian points of view, English as a lingua franca and Asian languages as a lingua vicinas (languages of neighbours) should be in the college curriculum. The notion of English as lingua franca that emphasizes communication rather than grammatical correctness suits the situation where Japanese non-native English teachers teach students. There is no such thing as a perfect speaker of any language. Those who have content—here, what they want to convey to younger users of English as a lingua franca—are all quali ed to teach English